AbstractIn 2016, a massive fish kill of the planktivorous pond smelt Hypomesus nipponensis occurred in Lake Suwa, Japan. Pond smelt, which is important fish species from commercial and cultural perspectives, influences the zooplankton community in the lake. Following the massive fish kill, Daphnia galeata appeared and their population density increased to previously unseen levels by summer 2017. To help recover the fish population, larval pond smelt were released into the lake. Consequently, D. galeata has rarely appeared in Lake Suwa since summer 2017, except for a low‐density population observed in May–June 2018. These phenomena indicated that fish predation is a possible primary factor for suppressing daphnid populations in shallow eutrophic lake. Zooplankton populations showed species‐specific responses to the alterations in predation pressure. When the D. galeata population peaked after the fish kill event, rotifers, which are small‐sized competitors of daphnids, and calanoids tended to decrease in density. Rotifers then increased with the decrease in the daphnid populations due to the recovery of fish. Alternatively, cyclopoids, which demonstrated a similar population density following the fish kill event, tended to decrease when the fish population recovered. The population densities of Leptodora cf. kindtii/richardi and Bosmina spp. did not significantly differ between before the massive kill event and after pond smelt recovery. It is believed that the changes in zooplankton population densities observed in the present study may provide insights for further monitoring of aquatic food webs in eutrophic water systems, including Lake Suwa, where re‐oligotrophication is occurring and biological interactions are changing.